Job ID = 1293842 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,384,399 reads read : 27,384,399 reads written : 27,384,399 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:13 27384399 reads; of these: 27384399 (100.00%) were unpaired; of these: 16532158 (60.37%) aligned 0 times 4509534 (16.47%) aligned exactly 1 time 6342707 (23.16%) aligned >1 times 39.63% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4677122 / 10852241 = 0.4310 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 02:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 02:55:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:55:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 02:55:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:55:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 02:55:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:55:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:55:58: 1000000 INFO @ Mon, 03 Jun 2019 02:55:58: 1000000 INFO @ Mon, 03 Jun 2019 02:56:00: 1000000 INFO @ Mon, 03 Jun 2019 02:56:07: 2000000 INFO @ Mon, 03 Jun 2019 02:56:07: 2000000 INFO @ Mon, 03 Jun 2019 02:56:10: 2000000 INFO @ Mon, 03 Jun 2019 02:56:15: 3000000 INFO @ Mon, 03 Jun 2019 02:56:15: 3000000 INFO @ Mon, 03 Jun 2019 02:56:20: 3000000 INFO @ Mon, 03 Jun 2019 02:56:23: 4000000 INFO @ Mon, 03 Jun 2019 02:56:23: 4000000 INFO @ Mon, 03 Jun 2019 02:56:29: 4000000 INFO @ Mon, 03 Jun 2019 02:56:31: 5000000 INFO @ Mon, 03 Jun 2019 02:56:31: 5000000 INFO @ Mon, 03 Jun 2019 02:56:39: 6000000 INFO @ Mon, 03 Jun 2019 02:56:39: 5000000 INFO @ Mon, 03 Jun 2019 02:56:39: 6000000 INFO @ Mon, 03 Jun 2019 02:56:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:56:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:56:40: #1 total tags in treatment: 6175119 INFO @ Mon, 03 Jun 2019 02:56:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:56:40: #1 tags after filtering in treatment: 6175119 INFO @ Mon, 03 Jun 2019 02:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:56:40: #1 finished! INFO @ Mon, 03 Jun 2019 02:56:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:56:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:56:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:56:41: #1 total tags in treatment: 6175119 INFO @ Mon, 03 Jun 2019 02:56:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:56:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:56:41: #1 tags after filtering in treatment: 6175119 INFO @ Mon, 03 Jun 2019 02:56:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:56:41: #1 finished! INFO @ Mon, 03 Jun 2019 02:56:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:56:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:56:41: #2 number of paired peaks: 1718 INFO @ Mon, 03 Jun 2019 02:56:41: start model_add_line... INFO @ Mon, 03 Jun 2019 02:56:41: start X-correlation... INFO @ Mon, 03 Jun 2019 02:56:41: end of X-cor INFO @ Mon, 03 Jun 2019 02:56:41: #2 finished! INFO @ Mon, 03 Jun 2019 02:56:41: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 02:56:41: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 02:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.05_model.r WARNING @ Mon, 03 Jun 2019 02:56:41: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:56:41: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 02:56:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:56:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:56:41: #2 number of paired peaks: 1718 INFO @ Mon, 03 Jun 2019 02:56:41: start model_add_line... INFO @ Mon, 03 Jun 2019 02:56:41: start X-correlation... INFO @ Mon, 03 Jun 2019 02:56:42: end of X-cor INFO @ Mon, 03 Jun 2019 02:56:42: #2 finished! INFO @ Mon, 03 Jun 2019 02:56:42: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 02:56:42: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 02:56:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.10_model.r WARNING @ Mon, 03 Jun 2019 02:56:42: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:56:42: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 02:56:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:56:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:56:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:56:48: 6000000 INFO @ Mon, 03 Jun 2019 02:56:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:56:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:56:50: #1 total tags in treatment: 6175119 INFO @ Mon, 03 Jun 2019 02:56:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:56:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 02:56:50: #1 tags after filtering in treatment: 6175119 INFO @ Mon, 03 Jun 2019 02:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:56:50: #1 finished! INFO @ Mon, 03 Jun 2019 02:56:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:56:51: #2 number of paired peaks: 1718 INFO @ Mon, 03 Jun 2019 02:56:51: start model_add_line... INFO @ Mon, 03 Jun 2019 02:56:51: start X-correlation... INFO @ Mon, 03 Jun 2019 02:56:51: end of X-cor INFO @ Mon, 03 Jun 2019 02:56:51: #2 finished! INFO @ Mon, 03 Jun 2019 02:56:51: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 02:56:51: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 02:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.20_model.r WARNING @ Mon, 03 Jun 2019 02:56:51: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:56:51: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 02:56:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:56:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:57:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:57:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.10_summits.bed INFO @ Mon, 03 Jun 2019 02:57:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1861 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:57:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:57:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:57:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.05_summits.bed INFO @ Mon, 03 Jun 2019 02:57:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3458 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:57:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:57:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:57:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299923/SRX1299923.20_summits.bed INFO @ Mon, 03 Jun 2019 02:57:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。